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Reeling from the shocking discovery of Rodney McKay's fate, Colonel Sheppard and his team retreat to Atlantis to regroup. With Rodney not only in the hands of the Wraith, but apparently working for them, Atlantis faces a new danger - their own man, turned against them.

While Zelenka and Colonel Carter work frantically to crack the security protocols McKay embedded in Atlantis's computer system, Ronon revisits his past and finds much is changing on Sateda. Meanwhile, Queen Death prepares to make use of her most valuable prisoner; with Rodney still unaware of his true identity, the fate of Atlantis hangs in the balance...

“Oh, not good,” Zelenka said, and followed it in Czech with what sounded like something heartfelt. “We have systems shutting down — internal sensors, power to the weapons chair —”

“Get that thing shut down,” Lorne said.

“Yes, I am trying —”

“What the hell is going on?” Sheppard said, tearing up the stairs into the control room, wearing sweatpants tucked into the tops of his boots and a flannel shirt he hadn’t bothered to tuck in at all.

“This is Rodney’s work,” Zelenka said. “His programs are shutting down our security systems, and I cannot stop it. I am afraid we are going to lose the iris.”

“Security teams to the gateroom,” Sheppard said into his radio. “Sound a citywide alarm.” Salawi’s hands moved uncertainly over her keyboard, but it was only seconds before the alarm sounded. “Put me on citywide,” Sheppard said, and waited for Salawi’s quick nod before he went on. “This is Colonel Sheppard. Assume that as of now we are facing an attack by unknown hostiles who are trying to get through the Stargate. I want security teams on full alert —”

Zelenka breathed a curse in Czech, all the more alarming because his tone was hushed rather than heated. “The iris is shutting down...”

In the absence of Richard Woolsey, Steven Caldwell could claim seniority over Samatha Carter and John Sheppard on who's in command over Atlantis. John's rank is Lieutenant Colonel while Carter and Caldwell share the same rank of full Colonel, with Caldwell gaining the rank at least 2 years before Carter.

During the Raid on Atlantis, the Stargate shield is repeatedly called the iris when in the show it is always called the shield. The expedition also acts like without the ZPM, the Stargate shield won't work when they were able to run the Stargate shield off the naquadah generators the entire first season.

On page 283, Pat Meyers is briefly referred to as "he" despite being a woman. In the next paragraph, Meyers is correctly referred to as "she."

The F-302s depicted here have shields that protect them from enemy fire. However, F-302s in the series never had energy shields installed. They are also not described here as part of any system upgrade.